chr12-14540826-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024829.6(PLBD1):āc.496A>Gā(p.Met166Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000292 in 1,611,204 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_024829.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLBD1 | NM_024829.6 | c.496A>G | p.Met166Val | missense_variant | 4/11 | ENST00000240617.10 | NP_079105.4 | |
LOC101928317 | XR_001749015.2 | n.589-265T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLBD1 | ENST00000240617.10 | c.496A>G | p.Met166Val | missense_variant | 4/11 | 1 | NM_024829.6 | ENSP00000240617 | P1 | |
ENST00000655882.1 | n.604-265T>C | intron_variant, non_coding_transcript_variant | ||||||||
PLBD1 | ENST00000540572.1 | c.355A>G | p.Met119Val | missense_variant | 4/5 | 5 | ENSP00000438367 | |||
PLBD1 | ENST00000541618.1 | c.*153A>G | 3_prime_UTR_variant, NMD_transcript_variant | 3/6 | 5 | ENSP00000441278 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152252Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251196Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135772
GnomAD4 exome AF: 0.0000295 AC: 43AN: 1458952Hom.: 0 Cov.: 30 AF XY: 0.0000303 AC XY: 22AN XY: 725838
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152252Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74390
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 14, 2023 | The c.496A>G (p.M166V) alteration is located in exon 4 (coding exon 4) of the PLBD1 gene. This alteration results from a A to G substitution at nucleotide position 496, causing the methionine (M) at amino acid position 166 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at